Dear. Freesurfer team. I'd appreciate any advice from you.
When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different... Do you have any suggestions for fixing this error? Should I do 3dWarp -deoblique? Thank you so much. Best, Ji Won 2016-02-08 16:30 GMT-05:00 Ji Won Bang <kirsten...@gmail.com>: > Dear. Freesurfer team. > > Hi. > > I'm using freesurfer 4.5 version. > > While doing the motion correction, an error occurred. > > the command I used: > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun > $DATA_DIR/$SUBJECT/bold_decode/003 > > the error I have: > /home/jbang/Projects/replay/epi/replay01/bold_retino > 3dvolreg -verbose -dfile 025/fmc.mcdat -base > 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix > 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz > ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] > ++ Authored by: RW Cox > *+ WARNING: If you are performing spatial transformations on an oblique > dset, > such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, > or viewing/combining it with volumes of differing obliquity, > you should consider running: > 3dWarp -deoblique > on this and other oblique datasets in the same session. > See 3dWarp -help for details. > ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 > degrees from plumb. > ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz > ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees > from plumb. > ++ centers of base and input datasets are 9.09 mm apart > ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD > don't have same dimensions! > Input: nx=74 ny=74 nz=32 > Base: nx=74 ny=74 nz=33 > ** FATAL ERROR: perhaps you could make your datasets match? > ERROR: 3dvolreg > Invalid null command. > > I think it's because the volume size is different. > > The volume size for bold_retino is: number of slices 32 > The volume size for bold_decode: number of slices 33 > > What should I do to correct this error? > > Thank you for taking your time. > > Best, > Ji Won >
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